Project Summary/Abstract Incidence of gonorrhea, caused by Neisseria gonorrhoeae, is growing across the globe, and this pathogen is becoming increasingly untreatable. Transmission among groups where antibiotic exposure is high contributes to the development of resistance in N. gonorrhoeae. Antibiotic resistance often imposes a fitness cost on resistant bacteria; however, mutations elsewhere in the genome can compensate for this reduced fitness, allowing resistant lineages to successfully compete with susceptible lineages even in the absence of antibiotic exposure. To develop successful public health policies related to resistance, we must understand the emergence, maintenance, and transmission of antibiotic resistant lineages. We hypothesize that antibiotic resistance in N. gonorrhoeae is influenced by transmission among high risk demographic groups and epistatic interactions between resistance alleles and compensatory mutations. We will address this hypothesis in two aims focused on transmission networks and the genomic background, respectively. In Aim 1, we will characterize N. gonorrhoeae transmission networks using whole genome sequencing data of the pathogen and detailed patient metadata from a dense sample of gonorrhea infections in New York City from 2011 to 2015. Transmission networks will be constructed using genetic distances and collection dates of N. gonorrhoeae isolates. Using Bayesian phylogenetic analysis, we will reconstruct transmissions between demographic groups within New York City. Transmission between geographic locations will also be identified using publicly available N. gonorrhoeae genomic data. The results from this study will contribute to optimal strategies to slow local and global transmission of resistant gonorrhea. Aim 2 will address the acquisition and maintenance of antibiotic resistance alleles during the evolution of N. gonorrhoeae. First, we will use a rapid search method to identify the presence of known resistance alleles in all available N. gonorrhoeae genomic data. We will reconstruct the gains and losses of individual resistance alleles, and we will identify correlations between the presence of resistance alleles. Second, we will perform a genome wide association study to identify interactions between resistance alleles and the genomic background of resistant lineages in natural populations of N. gonorrhoeae. Significant associations will include potential enabling or compensatory mutations. These results will contribute to further studies of compensatory evolution in N. gonorrhoeae and identify new genes and pathways that can be used as targets for novel therapies. The proposed studies will be carried out as part of a postdoctoral fellowship at the Harvard T.H. Chan School of Public Health. The postdoctoral fellow will acquire technical skills related to genomic epidemiology and genome wide association studies as part of this project. Additionally, professional development courses will contribute to science communication, grant writing, and mentoring skills needed to become an independent scientist at an academic institution.